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Photo of Tobias Ambjörnsson

Tobias Ambjörnsson

Senior lecturer

Photo of Tobias Ambjörnsson

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory

Author

  • V. Iarko
  • E. Werner
  • L. K. Nyberg
  • V. Muller
  • J. Fritzsche
  • Tobias Ambjörnsson
  • Jason Beech
  • Jonas Tegenfeldt
  • K. Mehlig
  • F. Westerlund
  • B. Mehlig
Show all

Summary, in English

The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

Department/s

  • Computational Biology and Biological Physics - Undergoing reorganization
  • Solid State Physics
  • NanoLund: Centre for Nanoscience

Publishing year

2015

Language

English

Publication/Series

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)

Volume

92

Issue

6

Document type

Journal article

Publisher

American Physical Society

Topic

  • Nano Technology
  • Biophysics
  • Other Physics Topics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1539-3755